Tag: GOrilla

Evolution of lysine-specific demethylase 1 and REST corepressor gene families and their molecular interaction

The RCOR gene repertoire expanded in the ancestor of jawed vertebrates To understand the duplicative history of the RCOR genes, we reconstructed gene phylogenies with different taxonomic samplings. The first analysis aimed to understand the evolution of RCOR genes in vertebrates (Fig. 2), whereas in the second, our sampling effort included…

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The Biostar Herald for Monday, December 11, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, cmdcolin, and was edited by…

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Identification of constrained sequence elements across 239 primate genomes

De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…

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Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells | BMC Cancer

A. Bioinformatics analyzes Search strategy and study selection From April to June 2021, we read relevant and related publications in Medline, EMBASE, Web of Science, and Wanfang. The search term “NOX4” have been used. The articles that fit specified criteria were all added at once: (1) Participants were split into…

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Data for non-human primates

Data for non-human primates 0 Hi everyone, I have two questions regarding data/annotations (parallel to human) for non-human primates: The GENCODE gene annotation file provides very comprehensive gene annotation but GENCODE has files only for human and mouse. Can I find some parallel file for non-human primates from any resource?…

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What is the homology of rRNA between whales and human

The homology of rRNA between whales and humans has been studied in several papers. Arnason et al. found that the mitochondrial DNA (mtDNA) of the fin whale is similar to that of other mammals, including humans, with a high level of similarity in the D-loop region and the rRNA genes….

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Solved PLZ DO THIS IN RSTUDIO AND PLZ SHOW CODEWhen R reads

PLZ DO THIS IN RSTUDIO AND PLZ SHOW CODE When R reads the data, or say creates a model like Mass~Sex, it will compare the data that comes first in the alphabet to those that come after. So although your hypothesis may be males are heavier than females and you’d…

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Getting differentially expressed transcripts among primates from RNA-seq data

Getting differentially expressed transcripts among primates from RNA-seq data 0 Hi, I have RNA-seq data for a certain tissue type for human, chimpanzee, gorilla and orangutan and macaque. I am thinking to look into differentially expressed transcripts instead of differentially expressed genes (DEGs). For a reason, I was wondering if…

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An Interview with Fyodor Urnov

By Jonathan D. Grinstein, PhD Fyodor Urnov, PhD, is a pioneer in the field of genome editing and one of the scientists most invested in expanding the availability and utility of CRISPR-based therapies to the broadest possible population. He envisions a world in which genome editing can treat the nearly…

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Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Phuangkum, P., Lair, R. C. & Angkawanith, T. Elephant Care Manual for Mahouts and Camp Managers (FAO Regional Office for Asia and the Pacific, 2005). Google Scholar  Sukumar, R. The Asian Elephant: Ecology and Management (Cambridge University Press, 1992). Google Scholar  Bansiddhi, P., Brown, J. L., Thitaram, C., Punyapornwithaya, V….

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Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose

Ceballos, G., Ehrlich, P. R. & Raven, P. H. Vertebrates on the brink as indicators of biological annihilation and the sixth mass extinction. Proc. Natl Acad. Sci. USA 117, 13596–13602 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Ceballos, G., Ehrlich, P. R. & Dirzo, R. Biological annihilation via the…

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Cyberpunk 2077 Monowire: Best skills, Cyberware, and how to use it

The Cyberpunk 2077 Monowire is an acquired taste. It’s not the flashiest arm weapon in the game, or even the best in terms of raw damage, but it is the cherry on top of Cyberpunk’s revamped netrunner skill tree in Update 2.0.  While it’s not really sensible to make a…

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Generate Go client and server from OpenAPI 3 specs

#development #github #golang #reading-list 🔗 Generate Go client and server from OpenAPI 3 specs github.com This package contains a set of utilities for generating Go boilerplate code for services based on OpenAPI 3.0 API definitions. When working with services, it’s important to have an API contract which servers and clients…

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Cathie Wood’s Buying These 3 Stocks Hand Over Fist

Would you like to improve your stock-picking chops by learning from the pros? You could wait for the next round of disclosures that institutional investors are required to make four times per year, or you could look at what Cathie Wood and the family of exchange-traded funds she manages for…

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Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

Consensus MTG taxonomy across primates The BRAIN Initiative Cell Census Network26 generated high-resolution transcriptomic maps of the MTG in human, chimpanzee, gorilla, macaque and marmoset by applying single-nucleus transcriptomic (snRNA-seq) assays to samples isolated from between three and seven donor brains in each species (plate-based SMART-seq v4 (SSv4) for great…

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Enterprise generative AI: Take or shape?

Image source: 123RF “Take” “Take” refers to the traditional software-as-a-service (SaaS) model where you use the software “as is” off-the-shelf. There are various options available. They include: Public access: Access to closed tools like OpenAI’s ChatGPT may be viable for some organizations. It is also free (if you believe in…

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Generation and Maintenance of Primate Induced Pluripotent Stem Cells Derived from Urine

The present protocol describes a method to isolate, expand, and reprogram human and non-human primate urine-derived cells to induced pluripotent stem cells (iPSCs), as well as instructions for feeder-free maintenance of the newly generated iPSCs. Primate IPSCs are useful but often difficult to obtain due to ethical and technical issues….

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Illumina Or Pacific Biosciences? The Upstart Vs. The 800-Pound Gorilla (NASDAQ:ILMN)

gemphotography/iStock via Getty Images Investment Overview One is based in San Diego, the other in Menlo Park, Calif. One has a market cap valuation (at the time of writing) of $29bn, the other $3.1bn. One earned revenues of $4.6bn last year, the other only $128m. One recorded a net loss…

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New Research Unlocks Hidden Secrets of Primate Evolution

An international research consortium co-led by scientists from multiple universities has released a series of studies detailing new high-quality reference genomes from 50 primate species, 27 of which were sequenced for the first time. The findings offer fresh insights into primate evolution, speciation, genomic diversity, and the evolution of brain…

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Vertex, AlphaDev, Function Calling, Gorilla, and Falcon

The latest update, spanning from June 12th, 2023, highlights the recent advancements and announcements in the domains of data science, machine learning, and artificial intelligence. This week’s spotlight is on notable entities such as Google, OpenAI, UC Berkeley, and AWS. Generative AI Support on Vertex AI Is Now Generally Available…

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Reading DNA from 233 primate species sheds light on what defines the human species and how human diseases emerge | Science & Tech

The last common ancestor of people and chimpanzees roamed the Earth about seven million years ago. That may sound like a long time, but it’s about the same span that separates African elephants and Asian elephants, two species so similar that people often simply call them elephants. Biologist Tomàs Marquès…

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The Primate Genome Project unlocks hidden secrets of primate evolution

Genomic phylogeny of primates. Credit: Dong-Dong Wu. Researchers from Zhejiang University, Kunming Institute of Zoology, Northwest University, and Yunnan University, Aarhus University, and BGI-Research have jointly led a series of significant new studies are published in a special issue of the journal Science, and in papers in Nature Ecology &…

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Galileo Charts Data Quality Course-Correction for AI Teams

(delcarmat/Shutterstock) For several months, the Silicon Valley startup Galileo has been selling an AI-powered product designed to help correct data quality issues for natural language processing (NLP) models and applications. Today the company announced that it’s expanding that core product out to help data science teams correct data problems impacting…

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Ambitious genome project shows how humans fit with other mammals

Scientists on Thursday unveiled the results of a project comparing the genomes of 240 mammal species – from aardvarks and aye-ayes to zebus and zebras, as well as people – to trace evolutionary changes spanning 100 million years, pinpointing genetic traits widely shared and those more uniquely human. The findings…

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Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons

de La Torre, S., Snowdon, C. T. & Bejarano, M. Effects of human activities on wild pygmy marmosets in Ecuadorian Amazonia. Biol. Conserv. 94, 153–163 (2000). Article  Google Scholar  Turvey, S. T. & Crees, J. J. Extinction in the Anthropocene. Curr. Biol. 29, R982–R986 (2019). Article  CAS  PubMed  Google Scholar …

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Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article  CAS  PubMed  Google Scholar  Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….

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Extensive prevalence and significant genetic differentiation of Blastocystis in high- and low-altitude populations of wild rhesus macaques in China | Parasites & Vectors

Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524–8. Article  CAS  PubMed  PubMed Central  Google Scholar  Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2021;135:260–82. Article …

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Anti-Smad4 antibody KO Tested (ab110175)

Overview Product name Description Rabbit polyclonal to Smad4 Host species Rabbit Tested applications Species reactivity Reacts with: HumanPredicted to work with: Mouse, Rat, Sheep, Horse, Cow, Dog, Pig, Chimpanzee,…

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California’s ‘Lady In The Fridge’ Identified After Nearly 30 Years

Genealogical DNA has given a name to a long-unidentified California woman whose corpse was discovered nearly 30 years ago in a submerged refrigerator, authorities announced last week. The Jane Doe referred to for years as the “lady in the fridge” was 29-year-old mother-of-three Amanda Lynn Schumann Deza, according to a…

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California’s ‘Lady In The Fridge’ ID’d As Amanda Deza

Genealogical DNA has given a name to a long-unidentified California woman whose corpse was discovered nearly 30 years ago in a submerged refrigerator, authorities announced last week. The Jane Doe referred to for years as the “lady in the fridge” was 29-year-old mother-of-three Amanda Lynn Schumann Deza, according to a…

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Generating and characterizing primate iPSCs for evolutionary analyses

Generating and characterizing primate iPSCs for evolutionary analyses Generating and characterizing primate iPSCs for evolutionary analyses The similarities and differences between us and our closest relatives, the primates, have fascinated researchers for decades and evoked various approaches to better understand the underlying genotype-phenotype relationship. Starting with early comparisons of protein…

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Transcription factor binding sites are frequently under accelerated evolution in primates

Pooling-based phylogenetic inference of accelerated evolution In the current study, we introduce a novel software application, GroupAcc, which includes two pooling-based phylogenetic approaches with improved statistical power to infer weakly accelerated evolution. The key idea of GroupAcc is to group TFBSs by the bound transcription factor and then examine whether…

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Can somebody suggest website(s) where I can find longevity of organisms?

Can somebody suggest website(s) where I can find longevity of organisms? 0 Pardon me if this is not the right platform for this question, in which case I would request you to guide me. I have been working on a bioinformatic project to look for a potential associateship between longevity…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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python – How can I fix the dash bio error: devtools cannot load source map dashbio@1.0.1 bundle.js.map?

I am implementing a website in Python with Django framework and using django-plotly-dash to display data. I am trying to use dash_bio’s IGV feature to display some chromosome data, but when I attempt to call the functionality, I receive the following errors and the callback that returns ‘dashbio.igv’ is unable…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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Mutational Analysis of Mitochondrial tRNA Genes

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

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Ranking gene list for GOrilla gene ontology enrichment analysis

Ranking gene list for GOrilla gene ontology enrichment analysis 0 Hi, I did a differential expression analysis using RNA-seq data from control and gene knockdown cells. Now I have a DE gene list and I want to do a gene ontology enrichment analysis using GOrilla, but I am not sure…

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